Pinto was present at a news conference when the Costa Rican federation announced his departure on Thursday.
Pinto said he was leaving because of disagreements with unnamed members of his coaching staff. He said they asked that he be fired 1½ years ago.
"I slept with the enemy for 1½ years," Pinto said. "I had my differences with the staff. They don't share my style. I'm demanding. I want dedication and effort."
Pinto, a Colombian, is likely to be attractive to a club or national team after the Ticos emerged from a group with Italy, England and Uruguay, all former world champions. They were eliminated in the quarterfinals by Netherlands, losing 4-3 on penalties after the match was 0-0 after extra time.
Pinto has previously said he has heard enquiries from Ecuador, Venezuela and Peru to coach their national teams.
"I realised I would not be able to count on conditions to carry out my work," Pinto said on his website. "So it wasn't possible to reach an agreement" to renew his contract.
Eduardo Li, president of the Costa Rican Football Federation, said it could take up to three months to name a replacement. He said primary assistants Paulo Wanchope and Luis Marin would handle the team until then.
Information from The Associated Press was used in this report.